[gmx-users] Press Equilibration

[Justin A. Lemkul]

On 6/12/12 7:10 AM, rama david wrote:
>
> Hi Gromacs Friends,
>
> I did NPT for 100 ps with folowing parameter
>
> ; Temperature coupling is on
> tcoupl        = V-rescale    ; modified Berendsen thermostat
> tc-grps        = Protein Non-Protein    ; two coupling groups - more accurate
> tau_t        = 0.1    0.1    ; time constant, in ps
> ref_t        = 310     310    ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman    ; Pressure coupling on in NPT
> pcoupltype    = isotropic    ; uniform scaling of box vectors
> tau_p        = 2.0        ; time constant, in ps
> ref_p        = 1.0        ; reference pressure, in bar
>
>
> I got foolowing result by using g_energy
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                   -3.99675       0.66    518.604   -2.89716  (bar)
>
>
> Is it is right??
> Is the system is equilibrated or I need to give more time ?????
>
>

Pressure is very hard to converge and often requires more than 100 ps.  There 
are numerous discussions on this topic, so please refer to the list archive for 
many useful posts.  Your pressure value is basically 4 ± 519.  Is that 
significantly different from 1?  No, likely not, but you can achieve a value of 
1 or very close if you equilibrate for a sufficiently long time.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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